CroCoNet

CroCoNet constructs comparable network modules centered on known transcriptional regulators and quantifies the variability in module topology within and between species to distinguish true evolutionary divergence from technical and biological confounders.

Key Features:

• Quantitative cross-species GRN comparison: CroCoNet quantitatively compares gene regulatory networks across species rather than relying on qualitative approaches.
• Conserved and diverged module identification: CroCoNet identifies network modules that are conserved or diverged between species.
• Confounder discrimination: CroCoNet distinguishes true evolutionary divergence from technical and biological confounders by contrasting variability levels within and between species.
• Transcriptional regulator-centered module construction: CroCoNet builds comparable network modules centered on known transcriptional regulators.

Scientific Applications:

• Cross-species regulatory rewiring detection: CroCoNet resolves regulatory rewiring across closely related species, as demonstrated by identifying divergent POU5F1 (OCT4) module topology despite conserved expression patterns.
• GRN evolution studies: CroCoNet provides a framework for studying gene regulatory network evolution using single-cell RNA-seq data from multiple species.
• Species-specific regulatory element analysis: CroCoNet findings can be integrated with analyses of species-specific genomic elements such as LTR7 elements to investigate contributions to network topology differences.

Methodology:

CroCoNet constructs comparable network modules centered on known transcriptional regulators, quantifies module topology variability within and between species, and contrasts these variability levels to distinguish true evolutionary divergence from confounders. The method was validated using cross-species CRISPRi perturbations coupled with single-cell RNA-seq as a readout.